Walnut (Juglans regia L.) is an important oilseed crop, and salt stress threatens the growth of walnut tree. In this study, NO3− or NH4+ was applied at three concentrations (4, 32, and 100 mM) to investigate the effect of NO3−-N and NH4+-N on walnut seedlings under 100 mM NaCl stress. Results showed that moderate (32 mM) NO3−-N application alleviated the effect of salt stress. Moreover, plants treated with 32 mM NO3−-N showed no significant morphological difference from those subjected to the nonstress treatment. The treatment of 32 mM NO3−-N application enhanced plant growth, increased antioxidant enzyme activities (superoxide dismutase and catalase), and restricted Na⁺ and Cl⁻ uptake and transport. Additionally, it might induce beneficial shifts in the rhizosphere microbiome. Low-concentration (4 mM) NO3⁻ or NH4⁺ treatment individually induced the minor alleviation of salt stress. By contrast, 100 mM NO3⁻ and all tested concentrations of NH₄⁺ further inhibited biomass and root growth, thereby exacerbating salt injury. Notably, 100 mM NH₄⁺ caused severe defoliation and seedling mortality. Furthermore, in contrast to its NO3− counterpart, 32 mM NH4⁺ shifted the root microbiome and impaired microbial diversity, likely contributing to increased salt sensitivity. This study demonstrates that moderate NO3⁻ application can effectively mitigate salt stress during walnut growth, offering a potential strategy for fertilizing walnut plantations under saline conditions.